rs2070767

chr22-23895276-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038911.1(MIF-AS1):n.626A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 802,300 control chromosomes in the GnomAD database, including 243,932 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.78 (46334 hom., cov: 30)
  • Exomes 𝑓: 0.78 (197598 hom.)
• Consequence: MIF-AS1 NR_038911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

Genes affected

MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)

MIF (HGNC:7097): (macrophage migration inhibitory factor) This gene encodes a lymphokine involved in cell-mediated immunity, immunoregulation, and inflammation. It plays a role in the regulation of macrophage function in host defense through the suppression of anti-inflammatory effects of glucocorticoids. This lymphokine and the JAB1 protein form a complex in the cytosol near the peripheral plasma membrane, which may indicate an additional role in integrin signaling pathways. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIF-AS1	NR_038911.1	n.626A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.626A>G		non_coding_transcript_exon_variant	3/3	1
MIF	ENST00000465752.1			downstream_gene_variant		1
MIF	ENST00000498385.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118618 AN: 151868 Hom.: 46290 Cov.: 30

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.768

GnomAD3 exomes AF: 0.784 AC: 115256 AN: 146996 Hom.: 45290 AF XY: 0.784 AC XY: 62212 AN XY: 79326

Gnomad AFR exome AF: 0.789

Gnomad AMR exome AF: 0.810

Gnomad ASJ exome AF: 0.744

Gnomad EAS exome AF: 0.672

Gnomad SAS exome AF: 0.820

Gnomad FIN exome AF: 0.807

Gnomad NFE exome AF: 0.778

Gnomad OTH exome AF: 0.794

GnomAD4 exome AF: 0.778 AC: 505886 AN: 650314 Hom.: 197598 Cov.: 8 AF XY: 0.779 AC XY: 269411 AN XY: 345700

Gnomad4 AFR exome AF: 0.792

Gnomad4 AMR exome AF: 0.808

Gnomad4 ASJ exome AF: 0.742

Gnomad4 EAS exome AF: 0.658

Gnomad4 SAS exome AF: 0.821

Gnomad4 FIN exome AF: 0.806

Gnomad4 NFE exome AF: 0.776

Gnomad4 OTH exome AF: 0.779

GnomAD4 genome AF: 0.781 AC: 118716 AN: 151986 Hom.: 46334 Cov.: 30 AF XY: 0.784 AC XY: 58229 AN XY: 74296

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.764

Alfa AF: 0.776 Hom.: 25730

Bravo AF: 0.781

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.1
Dann	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2070767; hg19: chr22-24237463; COSMIC: COSV53158711;